Variant report

Variant	rs624700
Chromosome Location	chr1:62900812-62900813
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:62899604-62903300	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:62899934-62903502	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:62900764-62902188	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:62900749-62900912	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:62899936-62903273	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:62899313-62903762	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:62900769-62901161	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:62900376-62903500	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:62899587-62903359	Raji	blood:	n/a	n/a
10	POLR2A	chr1:62900749-62903423	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:62900730-62900949	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:62899352-62904806	K562	blood:	n/a	n/a
13	POLR2A	chr1:62900801-62903204	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:62899539..62901299-chr1:62907455..62909142,2	MCF-7	breast:
2	chr1:53793068..53794573-chr1:62900533..62902613,2	MCF-7	breast:
3	chr1:62190320..62192154-chr1:62900473..62901978,2	MCF-7	breast:

Variant related genes	Relation type
USP1	TF binding region
ENSG00000162604	Chromatin interaction
ENSG00000225675	Chromatin interaction
ENSG00000157193	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002687	0.82[ASN][1000 genomes]
rs10889330	0.84[ASN][1000 genomes]
rs10889331	0.84[ASN][1000 genomes]
rs10889332	0.82[ASN][1000 genomes]
rs11207969	0.86[ASN][1000 genomes]
rs11207974	0.82[ASN][1000 genomes]
rs11588261	0.86[ASN][1000 genomes]
rs1167996	0.84[ASN][1000 genomes]
rs1167998	0.84[ASN][1000 genomes]
rs1168001	0.84[ASN][1000 genomes]
rs1168002	0.84[ASN][1000 genomes]
rs1168003	0.84[ASN][1000 genomes]
rs1168009	0.84[ASN][1000 genomes]
rs1168010	0.84[ASN][1000 genomes]
rs1168026	0.82[ASN][1000 genomes]
rs1168027	0.82[ASN][1000 genomes]
rs1168028	0.82[ASN][1000 genomes]
rs1168029	0.82[ASN][1000 genomes]
rs1168030	0.82[ASN][1000 genomes]
rs1168031	0.81[ASN][1000 genomes]
rs1168032	0.82[ASN][1000 genomes]
rs1168034	0.82[ASN][1000 genomes]
rs1168036	0.82[ASN][1000 genomes]
rs1168040	0.82[ASN][1000 genomes]
rs1168042	0.81[ASN][1000 genomes]
rs1177541	0.81[ASN][1000 genomes]
rs1183260	0.82[ASN][1000 genomes]
rs1184865	0.82[ASN][1000 genomes]
rs12023489	0.86[ASN][1000 genomes]
rs12029068	0.88[ASN][1000 genomes]
rs12124281	0.81[ASN][1000 genomes]
rs1305520	0.85[ASN][1000 genomes]
rs1305521	0.81[ASN][1000 genomes]
rs1690761	0.81[ASN][1000 genomes]
rs583609	0.86[ASN][1000 genomes]
rs597076	0.86[ASN][1000 genomes]
rs597078	0.86[ASN][1000 genomes]
rs597470	0.86[ASN][1000 genomes]
rs598253	0.86[ASN][1000 genomes]
rs624660	0.86[ASN][1000 genomes]
rs626787	0.89[ASN][1000 genomes]
rs630144	0.86[ASN][1000 genomes]
rs631106	0.89[ASN][1000 genomes]
rs634341	0.86[ASN][1000 genomes]
rs636497	0.86[ASN][1000 genomes]
rs637723	0.87[ASN][1000 genomes]
rs638305	0.88[ASN][1000 genomes]
rs641540	0.88[ASN][1000 genomes]
rs642845	0.84[ASN][1000 genomes]
rs656297	0.88[ASN][1000 genomes]
rs6587976	0.84[ASN][1000 genomes]
rs659656	0.86[ASN][1000 genomes]
rs7547965	0.85[ASN][1000 genomes]
rs783291	0.86[ASN][1000 genomes]
rs9436221	0.84[ASN][1000 genomes]
rs9436222	0.83[ASN][1000 genomes]
rs9436223	0.88[ASN][1000 genomes]
rs9436661	0.88[ASN][1000 genomes]
rs9988450	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs624700	DOCK7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62890600-62901000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:62891000-62901000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:62891000-62901000	Weak transcription	NHEK	skin
4	chr1:62895000-62901000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:62895600-62901000	Weak transcription	HSMMtube	muscle
6	chr1:62899800-62901000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:62899800-62901000	Weak transcription	NHDF-Ad	bronchial
8	chr1:62900000-62901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:62900000-62901000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:62900000-62901000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:62900000-62901000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:62900000-62901000	Weak transcription	HSMM	muscle
13	chr1:62900200-62901000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:62900200-62901000	Weak transcription	Fetal Heart	heart
15	chr1:62900200-62901000	Enhancers	HepG2	liver
16	chr1:62900200-62901200	Enhancers	Fetal Muscle Leg	muscle
17	chr1:62900400-62901000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:62900400-62901200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62900400-62901200	Enhancers	Lung	lung
20	chr1:62900400-62901400	Enhancers	Gastric	stomach
21	chr1:62900400-62904200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:62900600-62901000	Enhancers	Primary B cells from cord blood	blood
23	chr1:62900600-62901000	Enhancers	K562	blood
24	chr1:62900600-62901200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr1:62900600-62901200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:62900800-62901000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:62900800-62901000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:62900800-62901000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:62900800-62901000	Enhancers	Primary T cells from cord blood	blood
30	chr1:62900800-62901000	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:62900800-62901000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:62900800-62901000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:62900800-62901000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:62900800-62901000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:62900800-62901000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:62900800-62901000	Enhancers	Adipose Nuclei	Adipose
37	chr1:62900800-62901000	Enhancers	Liver	Liver
38	chr1:62900800-62901000	Enhancers	Brain Angular Gyrus	brain
39	chr1:62900800-62901000	Enhancers	Brain Anterior Caudate	brain
40	chr1:62900800-62901000	Enhancers	Brain Hippocampus Middle	brain
41	chr1:62900800-62901000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:62900800-62901000	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:62900800-62901000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:62900800-62901000	Enhancers	Fetal Brain Male	brain
45	chr1:62900800-62901000	Enhancers	Fetal Intestine Small	intestine
46	chr1:62900800-62901000	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:62900800-62901000	Enhancers	Fetal Thymus	thymus
48	chr1:62900800-62901000	Enhancers	Pancreas	Pancrea
49	chr1:62900800-62901000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr1:62900800-62901000	Enhancers	Rectal Smooth Muscle	rectum

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